ezMethodTrim: Trims input reads

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Trims input reads

Description

Trims input reads. The trimming happens in the following order:

• adapter

• quality window

• avg quality

• minimum length

• fixed trimming

This means if you specify a fixed trimming this comes on top of the adaptive trimming

Usage

ezMethodTrim(input = NA, output = NA, param = NA)

Arguments

input	a list, file path or an object of the class EzDataset containing the input.
output	an object of the class EzDataset or NA. If it is NA, it will be copied from the input.
param	a list of parameters: paired a logical specifying whether the samples have paired ends. subsampleReads an integer specifying how many subsamples there are. This will call ezMethodSubsampleReads() if > 1. trimAdapter a logical specifying whether to use a trim adapter. minTailQuality an integer specifying the minimal tail quality to accept. Only used if > 0. minTrailingQuality an integer specifying the minimal trailing quality to accept. Only used if > 0. minAvgQuality an integer specifying the minimal average quality to accept. Only used if > 0. minReadLength an integer specifying the minimal read length to accept. dataRoot a character specifying the path of the data root to get the full column paths from.

Value

Returns the output after trimming as an object of the class EzDataset.

Author(s)

Rehrauer, Hubert

Schmid, Peter

uzh/ezRun documentation built on April 24, 2024, 4:01 p.m.